annotate picard_DownsampleSam.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>Downsample a file to retain a subset of the reads</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    picard
    DownsampleSam
      --INPUT '$escaped_element_identifier'
      --OUTPUT '${outFile}'
      --PROBABILITY ${probability}
      --RANDOM_SEED ${seed}
      --QUIET true
      --VERBOSITY ERROR
      --VALIDATION_STRINGENCY ${validation_stringency}
  ]]></command>
    <inputs>
        <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset"/>
        <param name="probability" type="float" min="0.0" max="1.0" value="1" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads"/>
        <param name="seed" type="integer" value="1" label="Random seed value" help="RANDOM_SEED; default=1"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam"/>
            <param name="probability" value="0.1"/>
            <param name="seed" value="1024"/>
            <param name="validation_stringency" value="LENIENT"/>
            <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam" lines_diff="2"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.

@dataset_collections@

@description@

  INPUT=File
  I=File              The input SAM or BAM file to downsample.  Required.

  OUTPUT=File
  O=File              The output, downsampled, SAM or BAM file to write.  Required.

  RANDOM_SEED=Long
  R=Long              Random seed to use if reproducibilty is desired.  Setting to null will cause multiple
                      invocations to produce different results.

  PROBABILITY=Double
  P=Double            The probability of keeping any individual read, between 0 and 1.



@more_info@
  </help>
    <expand macro="citations"/>
</tool>